NAME¶

ipig - Integrating PSMs Into Genome browser visualizations

SYNOPSIS¶

ipig <psm file> |-g|-c|-cg [<config file>]

DESCRIPTION¶

iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/).

iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or in text format and provides results in genome track formats (BED and GFF3 files), which can be easily imported into genome browsers.

OPTIONS¶

<psm file>

indicates the file with the peptide spectrum matches (mzid/txt)

-g, -gui

starts the graphical user interface of iPiG

-c, -control

starts the gene control, necessary files have to be indicated in the configuration file

-cg, -controlgui

starts the graphical user interface of the gene control

-d, -downloader

starts the download gui

<config file>

a different configuration file can be indicated (otherwise ipig.conf is loaded by default)

additional requirements:

using a non-gui mode, a config file (ipig.conf by default) has to contain several additional parameters, e.g. indicating the reference genome etc.

in a gui mode (-g and -cg), additional parameters can be indicated two ways, within the interface or with a config file as well.

have a look into readme.txt and ipig.conf for examples and more details about the additional parameters